BwUniCluster2.0/Software/R/terra

Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)! UNDER CONSTRUCTION!!!

General information

terra is a R package for spatial data analysis with vectors (points, lines, polygons) and raster (grid) data.

sf is a R package that provides simple feature access for R.

In order to install those, we need to fulfill the following system requirements:

• GDAL 2.2.3 or higher
• PROJ 4.9.3 or higher
• GEOS 3.4.0 or higher

These packages are not available centrally on the cluster, but can be installed manually (to the $HOME-directory). Specifically, to install these packages, they need to be built from source.

Installation

Please enter (or copy & paste) the code, presented in the boxes below, directly into your shell/command line on bwUniCluster. The whole process will take approximately 45 minutes.

First, for compilation we obtain an interactive session (on a compute node):

# Obtain interactive session
salloc -n 8 -t 60 -p single

Preparations

Prepare an .R/Makevars file (if it does not already exists). This file specifies how R should compile the packages (i.e., sets some 'compiler flags').

If an .R/Makevars file is present in your home directory ($HOME), check whether the flags displayed below are already set and apply adjustments, if necessary:

# Ensure that the ~/.R/Makevars file has the following lines:
cat $HOME/.R/Makevars

CXX14=g++
CXX17=g++
CXX14FLAGS += -std=c++14
CXX17FLAGS += -std=c++17
CXXFLAGS = -O3 -fPIC -march=cascadelake -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option

Please run the following lines of code to set the flags, if necessary:

mkdir -p ~/.R
echo "CXX14=g++" > ~/.R/Makevars
echo "CXX17=g++" >> ~/.R/Makevars
echo "CXXFLAGS = -O3 -fPIC -march=cascadelake -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option" >> ~/.R/Makevars
echo "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars
echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars

Next, we create the directories for the source code and installation targets, respectively. Furthermore, we load all (software) modules relevant for compilation and ensure that the compilers are found:

# We install the libraries into the ~/sw/R directory.
mkdir -p ~/sw/R

# Source directory.
mkdir -p ~/src

# Load required modules.
module purge
module load devel/cmake/3.29.3
module load devel/python/3.12.3_gnu_13.3

# Check that the GNU compiler 13.3 is loaded.
gcc --version

# Set compiler for cmake and make.
export CC=$(which gcc)
export CXX=$(which g++)

The Python 3.12.3 module is missing some required packages which are included in the Python default module. Therefore, we install them in the user environment:

pip3 install --user numpy setuptools

Install external programs

First, we download the sources of GDAL, PROJ, GEOS (and their dependencies) and install them:

Install PROJ

# Download and unpack the PROJ source code:
PROJ_VER=9.4.1
cd $HOME/src
wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz
tar xf proj-$PROJ_VER.tar.gz

cd proj-$PROJ_VER
mkdir build && cd build

# Compile and install PROJ:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" ..
cmake --build . -j 8
cmake --build . --target install

Install GDAL

Building GDAL requires newer versions of OpenEXR and libdeflate then available on the system.

# Download and unpack the OpenEXR source code:
OPENEXR_VER=3.3.1
cd $HOME/src
wget https://github.com/AcademySoftwareFoundation/openexr/releases/download/v$OPENEXR_VER/openexr-$OPENEXR_VER.tar.gz
tar xf openexr-$OPENEXR_VER.tar.gz

cd openexr-$OPENEXR_VER/
mkdir build && cd build

# Compile OpenEXR:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" -DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install


# Download and unpack the libdeflate source code:
cd $HOME/src
git clone https://github.com/ebiggers/libdeflate

cd libdeflate
mkdir build && cd build

# Compile libdeflate
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
      -DCMAKE_PREFIX_PATH="$HOME/sw/R" \
      -DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install

Now, all necessary dependencies are available and we can build GDAL:

# Download and unpack the GDAL source code:
cd $HOME/src
GDAL_VER=3.9.3
wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz
tar xf gdal-$GDAL_VER.tar.gz

cd gdal-$GDAL_VER
mkdir build && cd build

cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
      -DCMAKE_PREFIX_PATH="$HOME/sw/R" \
      -DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install

Install GEOS

The last package that needs to be compiled is GEOS:

# Download and unpack the GEOS source code.
cd $HOME/src
GEOS_VER=3.13.0
wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2
tar xf geos-$GEOS_VER.tar.bz2


cd geos-$GEOS_VER
mkdir build && cd build

# Compile GEOS:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
      -DCMAKE_PREFIX_PATH="$HOME/sw/R" \
      -DCMAKE_BUILD_TYPE=Release ..
make -j 8
ctest -j 8
make install

Installing the R packages

In order to install the two R packages, we need to inform R where to find PROJ, GDAL and GEOS, so we export the necessary paths:

export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal

Additionally, the R package installation features compilation of built-in C++ code, for which we specify compilation options ('compiler flags')

export CFLAGS=-I$HOME/sw/R/include
export CXX="{$(which g++)} -std=c++11"
export CXX17=$(which g++)

Now, we install terra and sf from within R.

module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3


R -q
R> install.packages("terra")
R> library(terra)
terra 1.7.71


R> install.packages("sf")
R> library(sf)
Linking to GEOS 3.12.1, GDAL 3.8.3, PROJ 9.3.1; sf_use_s2() is TRUE

Preparations to use the terra and sf packages

Since terra and sf depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.

We recommend to add the export commands

export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal

to your batch job scripts that use terra and sf or to run them directly in the command line if you use an interactive session.